BioImaging Hub
NALMIN Oslo Nodes received Funding to set up BioImaging eInfrastructure for Microscopy Image Processing and Image Storage.
Three imaging core facilities(BioImaging Hub Nodes) in UiO has received 3.8 million NOK from UiO central IT department USIT to set up IT infrastructures for image processing and image storage. The three initial BioImaging Hub nodes are: KlinkMed Shared Facility (NALMIN Oslo Node), IBV Shared Facility (NALMIN Oslo Node, NorMIC) and IMB Shared facility.
P1: The server admin(Harold) and the project coordinator(Edna) of the BioImaging Hub
The following IT infrastructure will be implemented with the support of this funding for the next three years(starting from Jan 2022):
A). local image processing workstations for each node,
B). a cloud based, FAIR principle compatible image data storage server
C). and a centralized remote accessible image processing server.
P2: NorMIC Image Processing Workshop.
7th NorMIC Workshop:
Methods in Optical Microscopy (and 3D Printing for Microscopes)
16th to 19th Nov 2021, UiO
Tentative Program of the Workshop
(Seminar Open to All, receive zoom link by emailing xian.hu at ncmm.uio.no)
The NorMIC series of workshops aims to teach biological researchers (PhD students, engineers, postdocs and young PIs) the principles of biological microscopes and image processing.
Bioimaging has become a potent and popular tool for biological researchers. However, many biologists who regularly use imaging don’t fully understand the basic principles of how the technology works. This can cause issues as, unlike other techniques such as a Western Blot, mistakes made in bioimaging are not readily obvious to the untrained eye. Correctly processing recorded images can hence cause issues if the researcher has not been extensively trained.
The NorMIC series of workshops aims to teach biological researchers (PhD students, postdocs, and young PIs) the principles of biological microscopy and image processing, and to educate them on the pros and cons of different types of microscopes and processing algorithms, and introduce them to the potential artifacts inherent to the technology.
The workshop, organised by NCMM and Oddmund Bakke, Department of Life Sciences, UiO will cover the basics of optical microscope image formation, common artifacts, and many popular state of the art imaging techniques (SMLM, SIM, expansion microscopy, 2P imaging, FRET, FRAP etc). All are taught with an emphasis on image processing. We will cover the key techniques used for image processing alongside the common tools that are either free for researchers to use or available at the University of Oslo and Oslo University Hospital’s shared facilities.
With the revolution of bringing 3D printers to the masses, people have started getting creative in manufacturing and at home. These devices find their way into scientific areas, where researcher can fabricate customized labware in order to make everyday lab life easier. The apparent variety of types of printers and properties of printing materials might be intimidating for beginners. In this special edition of the NorMIC workshop, we will spend a few lectures covering the knowledge required to start 3D printing in your own laboratory.
In the last years, the open community of microscopy started putting efforts into making cutting-edge microscopes available to everybody by making use of 3D printers in combination with sharable CAD designs, Raspberry Pi cameras, and low-cost objective lenses. The second part of the 3D printing session in this workshop will give you an overview of what is there, how you can find resources to replicate and get your hands “dirty” while designing some parts for your microscope. Ultimately, we will show you how the open-source modular optical toolbox “UC2” (https://github.com/openUC2/UC2-GIT) can help you making your biological imaging experiments as easy as using a Fiji plugin.
News Letter on 6th NorMIC Workshop
6th NorMIC Imaging Workshop
Course in Advanced Light Microscopy and Image Processing
The NorMIC series of workshops aims to teach biological researchers (PhD students, postdocs and young PIs) the principles of biological microscopes and image processing.
Time and place: May 25, 2021–May 28, 2021, IBV & Zoom
Bioimaging has become a potent and popular tool for biological researchers. However, many biologists that regularly use imaging don’t fully understand the basic principles of how the technology works. This can cause issues as, unlike other techniques such as a Western Blot, mistakes made in bioimaging are not immediately obvious to the untrained eye. Correctly processing generated images can also cause issues if the researcher has not been properly trained.
The NorMIC series of workshops aims to teach biological researchers (PhD students, postdocs and young PIs) the principles of biological microscopes and image processing, and to educate them about the pros and cons of different types of microscopes and processing algorithms, alongside the potential artefacts that might come with using the technology.
The workshop, organised by NCMM and Oddmund Bakke, Department of Life Sciences, UiO will cover the basics of optical microscope image formation, common artefacts, image data management with regards to the FAIR data principle. All are taught with an emphasis on image processing. We will cover the key techniques used in image processing alongside the common tools that are either free for researchers to use or available at the University of Oslo and Oslo University Hospital’s shared facilities.
Teaching will come from world-leading researchers
- Rainer Heintzmann, the co-inventor of Structured Illumination Microscopy (SIM) and Instant Structured Illumination Microscopy (iSIM). Rainer will demonstrate the powerful free deconvolution software developed in his lab.
- Anna Klemm, an image processing scientist and well-known Cell Profiler instructor. Anne has trained many of the imaging specialists in Oslo. View some of her work here.
- Romain F. Laine, a researcher from the Ricardo Henriques group, the group that invented SRRF stream.
- Stephen Cody, of Monash Micro Imaging. Stephen is famous for generating many powerful online teaching tutorials for microscopy and several auxiliary live imaging tools.
- Felix Margadant, a member of the Harald Stenmark group. Felix has devised several cellular force measurement tools. A software suite used in his UiO collaboration is
PC Cheng, Professor at the Department of Electrical Engineering, State University of New York in Buffalo, USA and famous plant biologist. Specialist in confocal microscopy, biomedical imaging, x-ray microscopy, microtomography, and lithography.
- PC Cheng and Felix Margadant are contributing authors to the book ‘Handbook of Biological Confocal Microscopy’ available here.
The topics that the course will cover include: image formation, processing workflow, segmentation, filters, de-convolution, rendering and visualization, classification, AI-based processing – see poster above for full details.
We will use the following software: Image J, Imaris, Cell Profiler, Nikon NIS, and Matlab.
Full list of teaching faculties involved:
- Rainer Heintzmann (University of Jena, Germany)
- Felix Margadant (Radium Hospital, Oslo University Hospital, Norway)
- Kay Schink (Radium Hospital, Oslo University Hospital, Norway)
- PC Cheng (State University of New York in Buffalo, USA)
- Anna Klemm (UPPSALA University, Sweden)
- Rafael Camacho (University of Gothenburg, Sweden)
- Korbinian Bösl (University of Bergen,Norway)
- Guergana Dontcheva (Bitplane.com, UK)
- Laura Rodriguez de la Ballina (Riks Hospital, Oslo University Hospital, Norway)
- Dominik Frei (Inter Instrument As, Norway)
- Frode Skjeldal (IBV, University of Oslo, Norway)
- Maria Àngeles Jimènez Sigstad (NCMM, University of Oslo, Norway)
- Øyvind Ødegaard Fougner (Radium Hospital, Norway)
- Edna, Xian Hu (NCMM, University of Oslo, Norway)
- Pia Larsson (Australian Centre for Blood Diseases, Monash University, Australia)
- Stephen Cody (Monash Micro Imaging, Australia)
- Romain F. Laine (Ricardo Henriques group, MRC LMCB, University College London, UK)
- Bjørnar Sporsheim (NTNU, Norway)
- Niklas Boknäs (Linköpings Universitet, Sweden)
Organizing Committee: Edna, Xian Hu; Oddmund Bakke ; Felix Margadant ; Kay Schink
Supporting Staff : Linda Haugen(IBV Invoicing), Elisa Bjørgo(NCMM Administration), Annabel Darby(NCMM Communication), Larissa Lily (NCMM Administration), Harold Gutch (NCMM IT) and Sabry Razick(UiO IT).
Due to server capacity for our lab sessions, the workshop can only host 70 participants. The registeration is closed as we have reached maximum capacity.
If you are interested to join the lectures please contact Annabel ( annabel.robertson at ncmm.uio.no) to receive the lecture zoom links.
Chart of distribution of registered students. A total of 7 students have been granted scholarship.